I was using my old UNO with an AVR Programmer, everything worked fine. Now I switched to the DUE and a J-Link JTAG. How can I upload my sketches directly with my programmer? With AVR I just needed to Choose one frome the menu, but there are no ARM Programmer yet. Any suggestions?

I already found the following document, but as far as I see it is for AVR programmer as well.http://arduino.cc/en/Hacking/Programmer